library(haemdata)
library(SummarizedExperiment)
use_pinboard("onedrive")Human datasets
Human datasets
First, setup the pin-board from which well retrieve the human datasets
City of Hope Biobank FLT3 patients
Patient metadata
Limited patient metadata are availalbe for these samples:
sample_id, patient_id, sex, diagnosis_year, clinical_treatment, date_of_diagnosis, age_at_diagnosis, sample_date
pca$biplot
pca$pairs_plot
pca$correlation_plot
Kim et al 2020 Sci Rep 
Bioproject: PRJEB27973
Pan-Cancer Panel
This dataset is TruSight RNA Pan-Cancer Panel (1385 genes) (Illumina, Inc., San Diego, CA USA). This is not a full transcriptome dataset.
Patient metadata
No further patient-level metadata was made available either via NCBI or the publication, although the supplementary tables contain extensive summary statistics. Contact the authors for more information.
pca$biplot
pca$pairs_plot
pca$correlation_plot
| Dataset | ID | Technology | Samples |
|---|---|---|---|
| EGAD00001003891 | Illumina | HiSeq 2500 | 266 |
Dataset Description
Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. A total of 211 patients were genotyped by targeted deep sequencing. For controls, bone marrow CD34+ cells and bone marrow mononuclear cells were obtained from three healthy adults each.
Patient metadata
No further patient-level metadata was made available either via EGA or the publication, although the supplementary tables contain extensive summary statistics. Contact the authors for more information.
Usage
Data were downloaded from EGA with approval and must not be used for any purpose other than PSON studies.
Shiozawa et al 2017 Blood 
Shiozawa et al 2018 Nat Comm 
pca$biplot
pca$pairs_plot
pca$correlation_plot
Non-AML patients sourced form a variety of studies:
- [PRJNA252189](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA252189) Transcriptomic profiling of peripheral blood mononuclear cells from healthy individuals
- [PRJNA261023](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA261023) Transcriptomic profiling of bone marrow cells from healthy individuals
- [PRJNA268220](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA268220) RNA sequencing of bone marrow CD34+ cells from myelodysplastic syndrome patients with and without SF3B1 mutation and from healthy controls
- [PRJNA294808](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA294808) Transcriptomes of peripheral blood mononuclear cells from a Guillain-Barre Syndrome patient and her healthy twin sampled at three different points of the disease evolution
- [PRJNA453199](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA453199) RNA sequencing analysis of adult mixed phenotype acute leukemia (MPAL)
- [PRJNA487456](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA487456) RNA-Seq of CD34+ Bone Marrow Progenitors from Healthy Donors
- [PRJNA493081](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA493081) Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry [bulk] pca$biplot
pca$pairs_plot
pca$correlation_plot
Show the code
mat_flt3 <- assay(flt3, "abundance")
mat_kim <- assay(kim, "abundance")
mat_mds <- assay(mds, "abundance")
mat_non_aml <- assay(non_aml, "abundance")
mat<-cbind(mat_flt3,
mat_kim,
mat_mds,
mat_non_aml)
row_data <- rowData(flt3)
col_flt3 <- colData(flt3)|>as.data.frame()
col_kim <- colData(kim)|>as.data.frame()
col_mds <- colData(mds)|>as.data.frame()
col_non_aml <- colData(non_aml)|>as.data.frame()
col_data <- dplyr::bind_rows(
col_flt3,
col_kim,
col_mds,
col_non_aml) |> DataFrame()
se <- SummarizedExperiment(assays = list("abundance"=mat), colData=col_data, rowData=row_data)
pca <- pca_se(se, col_by = "cohort")pca$biplot
pca$pairs_plot
pca$correlation_plot